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- EMDB-76080: DNA-guided AsCas12a -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76080
TitleDNA-guided AsCas12a
Map data
Sample
  • Complex: Cas12a:psiDNA:tarRNA
    • Protein or peptide: CRISPR-associated endonuclease Cas12a
    • RNA: Target RNA
    • DNA: psiDNA
KeywordsCRISPR-Cas12a / psi-DNA / Ternary Complex / Effector / RNA-binding / IMMUNE SYSTEM-RNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


Bacillus subtilis ribonuclease / deoxyribonuclease I / deoxyribonuclease I activity
Similarity search - Function
: / CRISPR-associated endonuclease Cpf1 REC2 domain / CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas12a
Similarity search - Component
Biological speciesAcidaminococcus sp. (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsFregoso Ocampo R / Taylor DW / Jain PK / Orosco C / West MW
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: An intricately folded guide RNA scaffold enables DNA targeting by the compact Cas9d nuclease
Authors: Fregoso Ocampo R / Bravo J / Das A / Nielsen S / Taylor DW
History
DepositionMar 14, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76080.png

Downloads & links

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Map

FileDownload / File: emd_76080.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.624 Å		0.83 Å/pix.
x 320 pix.
= 266.624 Å		0.83 Å/pix.
x 320 pix.
= 266.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.0013467 - 1.4251361
Average (Standard dev.)0.00029227382 (±0.02563955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76080_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76080_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cas12a:psiDNA:tarRNA

EntireName: Cas12a:psiDNA:tarRNA
Components
  • Complex: Cas12a:psiDNA:tarRNA
    • Protein or peptide: CRISPR-associated endonuclease Cas12a
    • RNA: Target RNA
    • DNA: psiDNA

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Supramolecule #1: Cas12a:psiDNA:tarRNA

SupramoleculeName: Cas12a:psiDNA:tarRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acidaminococcus sp. (bacteria)
Molecular weightTheoretical: 151.206 KDa

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Macromolecule #1: CRISPR-associated endonuclease Cas12a

MacromoleculeName: CRISPR-associated endonuclease Cas12a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I
Source (natural)Organism: Acidaminococcus sp. (bacteria)
Molecular weightTheoretical: 151.418953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT YADQCLQLVQ LDWENLSAAI DSYRKEKTE ETRNALIEEQ ATYRNAIHDY FIGRTDNLTD AINKRHAEIY KGLFKAELFN GKVLKQLGTV TTTEHENALL R SFDKFTTY ...String:
MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT YADQCLQLVQ LDWENLSAAI DSYRKEKTE ETRNALIEEQ ATYRNAIHDY FIGRTDNLTD AINKRHAEIY KGLFKAELFN GKVLKQLGTV TTTEHENALL R SFDKFTTY FSGFYENRKN VFSAEDISTA IPHRIVQDNF PKFKENCHIF TRLITAVPSL REHFENVKKA IGIFVSTSIE EV FSFPFYN QLLTQTQIDL YNQLLGGISR EAGTEKIKGL NEVLNLAIQK NDETAHIIAS LPHRFIPLFK QILSDRNTLS FIL EEFKSD EEVIQSFCKY KTLLRNENVL ETAEALFNEL NSIDLTHIFI SHKKLETISS ALCDHWDTLR NALYERRISE LTGK ITKSA KEKVQRSLKH EDINLQEIIS AAGKELSEAF KQKTSEILSH AHAALDQPLP TTLKKQEEKE ILKSQLDSLL GLYHL LDWF AVDESNEVDP EFSARLTGIK LEMEPSLSFY NKARNYATKK PYSVEKFKLN FQMPTLASGW DVNKEKNNGA ILFVKN GLY YLGIMPKQKG RYKALSFEPT EKTSEGFDKM YYDYFPDAAK MIPKCSTQLK AVTAHFQTHT TPILLSNNFI EPLEITK EI YDLNNPEKEP KKFQTAYAKK TGDQKGYREA LCKWIDFTRD FLSKYTKTTS IDLSSLRPSS QYKDLGEYYA ELNPLLYH I SFQRIAEKEI MDAVETGKLY LFQIYNKDFA KGHHGKPNLH TLYWTGLFSP ENLAKTSIKL NGQAELFYRP KSRMKRMAH RLGEKMLNKK LKDQKTPIPD TLYQELYDYV NHRLSHDLSD EARALLPNVI TKEVSHEIIK DRRFTSDKFF FHVPITLNYQ AANSPSKFN QRVNAYLKEH PETPIIGIDR GERNLIYITV IDSTGKILEQ RSLNTIQQFD YQKKLDNREK ERVAARQAWS V VGTIKDLK QGYLSQVIHE IVDLMIHYQA VVVLENLNFG FKSKRTGIAE KAVYQQFEKM LIDKLNCLVL KDYPAEKVGG VL NPYQLTD QFTSFAKMGT QSGFLFYVPA PYTSKIDPLT GFVDPFVWKT IKNHESRKHF LEGFDFLHYD VKTGDFILHF KMN RNLSFQ RGLPGFMPAW DIVFEKNETQ FDAKGTPFIA GKRIVPVIEN HRFTGRYRDL YPANELIALL EEKGIVFRDG SNIL PKLLE NDDSHAIDTM VALIRSVLQM RNSNAATGED YINSPVRDLN GVCFDSRFQN PEWPMDADAN GAYHIALKGQ LLLNH LKES KDLKLQNGIS NQDWLAYIQE LRN

UniProtKB: CRISPR-associated endonuclease Cas12a

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Macromolecule #2: Target RNA

MacromoleculeName: Target RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Acidaminococcus sp. (bacteria)
Molecular weightTheoretical: 12.216349 KDa
SequenceString:
GACAUUUAAC AACACCAGUC GAUGGGCUGU AGCAUAAA

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Macromolecule #3: psiDNA

MacromoleculeName: psiDNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Acidaminococcus sp. (bacteria)
Molecular weightTheoretical: 12.606116 KDa
SequenceString:
(DA)(DC)(DA)(DG)(DC)(DC)(DC)(DA)(DT)(DC) (DG)(DA)(DC)(DT)(DG)(DG)(DT)(DG)(DT)(DT) (DT)(DA)(DG)(DA)(DT)(DG)(DT)(DG)(DA) (DA)(DT)(DC)(DA)(DT)(DC)(DT)(DT)(DT)(DA) (DA) (DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 79.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 296277
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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